Copyright 2021 Emeline Favreau, University College London.

Objective of analysis

We tested each species againt a dataset comprising gene expression data for the five other species, or a lineage specific dataset (e.g. only bees). The SVM model gives the list of predictor genes (genes whose expression predicts the phenotype of a given sample), after Recursive Feature Selection (ie iteratively removing the weakest gene in predicting phenotype, running from 3718 orthogroups to 100).

Analysis steps:

  • Obtaining data
  • Aim 1-6: Plotting results from the leave-one-out analyses with a training set of 5 species
  • Aim 7-9: Plotting results from the leave-one-out analyses with a training set of bees only
  • Aim 10-12: Plotting results from the leave-one-out analyses with a training set of wasps only

Aim 1: Ceratina australensis trained on 5 species

The larger line is the average for a given phenotype: Reproductive (R) or Non-Reproductive (NR).

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image

Aim 2: Ceratina calcarata trained on 5 species

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image

Aim 3: Megalopta genalis trained on 5 species

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image

Aim 4: Liostenogaster flavolineata trained on 5 species

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image

Aim 5: Polistes canadensis trained on 5 species

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image

Aim 6: Polistes dominula trained on 5 species

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image

Aim 7: Ceratina australensis trained on bees

The training dataset comprises of only two species (the other two bees).

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image

Aim 8: Ceratina calcarata trained on bees

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image

Aim 9: Megalopta genalis trained on bees

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image

Aim 10: Polistes canadensis trained on wasps

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image

Aim 11: Polistes dominula trained on wasps

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image

Aim 12: Liostenogaster flavolineata trained on wasps

## `summarise()` has grouped output by 'phenotype'. You can override using the `.groups` argument.

## Saving 7 x 5 in image